Old Machines
by Yautja117
Summary: They are old. Long ago, a great civil war begun between them and the evil ones created the Reapers. Now, Shepard is thrust into the very heart of it.
1. Chapter 1: First Contact

Damn, it's been a long time since I've been on here. But the creative writing class I've got me back into the swing of things. I'm sorry to those who were following my Halo exploit. It just wasn't coming together. This will be a crossover. I'll let the story tell itself though. Enjoy and please review, so I know it's any good. I'm a bit rusty.

Chapter 1: First contact.

"Shepard, Shepard, Shepard…" thought Miranda sitting at her desk. It had been five days since they'd gone into Hell and back, losing no one. She knew better than anyone that Commander Shepard was good, but damn…

She hadn't had much to do lately, but sit and reflect on what had happened. Her loyalty to Mike Shepard had cost her greatly. The Illusive Man wasn't going to be happy about losing some of his most valuable assets. Miranda actually thought this situation was _funny. _No matter where they went, someone always knew Mike and always assumed he was gonna blow something up.

He was such a sweet guy…kind, caring, compassionate. Shepard was one of a kind. Around his crew, Mike would be an inspiration, a force of good nature unlike anything she'd ever scene and on the battle field be a brutish fighter that'd throw himself in harm's way for a fellow man. He was one hell of a good soldier and spokesmen though. She'd never seen anyone stir up a combat group like that before. Commander Shepard spoke to them like equals, all of them, even the Quarian.

Miranda reclined in her chair, truly relaxed for the first time in many years. Mike had been the best thing that'd ever happened to her. What was this feeling? Love? She certainly felt a pang on jealousy when she'd seen him talking to that Quarian…Tali.

This was so strange! He was so different! While she was generally cold and calculating, he was soft and playful! You were so comfortable around him. Shepard filled the room with this strange warmth. He radiated a power, but it wasn't violent or forceful.

Since they had gotten together, Miranda had forsaken her quarter's bed and began sleeping with Shepard. It was so comfortable, snuggling close to his bare, hard, warm chest under the loose covering blankets. After a few days though, she had begun noticing he almost never slept peacefully. He would sleep an hour or two, but then he'd talk to himself, silently screaming. She'd asked him and he said it was because of the beacon's effects from two year's prior. Miranda felt a small but terrible pang in her heart. It was the first time in many years this had happened to her.

Commander Mike Shepard, war hero and Good Samaritan to the universe, was up relaxing in his cabin. He could get used to this Normandy and its comforts. Soon enough it was back to the Citadel and the Council. This was…a nice little vacation. But he had to keep in shape, pushing himself and his team. The Reapers were coming and damn it, they were the only ones who knew it!

Miranda…that was another story. Two years ago, he'd have treated her like any other crew member. A nod here, a how ya doing there…Now? He cared about a lot about her… loved her. She was damned nice when you got to know her, which was tough.

He remembered her cold demeanor, the iciness of her voice when they first spoke. When was it, when he first started to care? Was it when they went to save Oriana? He didn't know.

The com. Buzzed and Joker's voice blared out "Um, Commander, you may want to come here. We're getting some strange readings. It doesn't match with any known ships. Not even Sovereign's"

"…Reapers?" he thought, leaping up from his desk and charging into the elevator.

Shepard, in mid elevator ride, paged Miranda on her Com. "Miranda, meet me at the helm. Some things up."

Her voice rang in, cool and collected "Right, Shepard. Know what's up?"

"No, Joker just paged me. An unknown signal, not even matching Reaper ships."

"Damn it, what now?" she muttered. Reapers…Collectors…how much else was out there, gunning for them? "Crap…now I'm starting to think like Garrus. She could really use some RnR with Shepard. Was a little break from all this really that much to ask for?

Shepard and Miranda met up, there was a quick peck on the lips, and headed towards the forward section of the ship.

"Joker, how close are we?" said Shepard, surveying the various monitors around the bridge.

"The vessels or whatever they were, just jumped…without a mass accelerator in the cluster! What the hell? EDI, what were those?" Joker belted out, a mixture of shock and awe written on his face.

"It is unknown, Jeff. Those vessels were of an unknown make and size, but had some serious chatter going on between them."

"Translate any of it? Better question, can they kill us or maim us in anyway?" said Joker, looking at the glowing blue ball of –oh-so-wonderful joy.

"Two words. And one of them matches nothing in my data bases. They are Reapers and…"

"And?" said Mike, looking over at EDI. Miranda crossed her arms impatiently.

"Decepticons?" said the ship, unsure about the word.

"Decepticons? Sounds like some ancient children show villain." Coughed Joker.

"Joker, this is serious. This tech is very advanced, maybe advanced as the Reapers." said Miranda.

"She's right, we've got to find out who they were. How the Reapers and them are connected." He shook his head wearily. Sometimes, saving the galaxy was a real pain in the ass. It was a tiring, nearly (by people that mattered) ignored. But the people of the galaxy really liked it when you when out of your way to help them. That's why he kept going, seeing the smile on the face of friends and strangers, it was totally worth it. Mike smiled to himself. He was going to post this with the Alliance, maybe they had something. But immediately after he mailed them, he was taking his team out somewhere nice. They deserved it after everything and he needed to recharge abit. He also wanted to take Miranda out somewhere, somewhere nice and quiet, so he could spend time with her that didn't involve blasting mercs and crushing intergalactic evil.

Maybe a nice little retreat on Illium. They'd been there several times, but it was always business. A few days to walk around and sight see, get a small breath of fresh air before plunging right back into the thick of it. His team deserved that much.

Since their assault on the Collector base, Samara, Thane and Legion had left the crew. Samara seemed reluctant, but duty called her elsewhere. She left Shepard her ping address, so if he got back into trouble, he could call on her aid. Thane went to visit his son on the Citadel, for Thane's illness had begun to claim its victim. Legion just chattered about returning to the Geth. Mike was sad to see them go. They were his crew, they helped him do the impossible. He would miss them.

Nearby, on a desolate world they waited by their leader's side. The ancient, giant machines stood inside their underground command hub, talking in their electronic language that was faster than light itself.

"It is time."

Okay, I know it wasn't very subtle what I was alluding too, but I have a few twists in mind. Please review, I know I'm abit rusty, so it probably sucks, but I like the input. Thank you.


	2. Chapter 2: First Meetings

Yay! Here's chapter 2. Please review, it helps me improve my writing and increase quality. Thank You.

Chapter 2: First meetings

There they were, a small fleet of ships floating in the vast void of space, hovering in the light of a star. Electronic, faster than light communications ran between them, highlighting their plans for this universe. They came from beyond this universe, from the beyond the rim of Dark Space.

At the head of the fleet was a massive blue and red freighter, with a small part of silver and red cruisers, a deep red frigate with massive weapons floated silently, with the others swarming about. A small yellow ship, moved lazily along, with no care in the world.

These ships had no crew. They were ancient, the hulls scarred from a thousand battles, worn and dented. Many had been welded dozens of times over, the refractive coating peeling up after twelve billion years of war. They were sentient and were looking for someone…someone named Shepard. Shepard had proved to be able to fight and protect others; he saved these creatures twice from the threat of extinction. But now the stakes were raising and no one noticed. The Reapers were only drones, robotic play thinks of much more masterful machines. He could be a key, instrumental in rallying this universe's inhabitants into a single unified force. This could be their only hope against the coming storm that threatened to consume and destroy all life in the universe.

Radio chatter. "Shepard, Michael L. located. Crescent Nebula, Tasale system, Terminus Systems."

"Illium? Strange name for a world."

The ship's began to produce a mass effect field and flashed. The ship's accelerated so quickly that they were no longer visible, to the naked eye.

Nearby, a small vessel, black as space returned to its master. "Objective located." said the drone to the larger machine. A hatch opened and the smaller machine linked into the system. Data on the enemy began to tumble into the net. The giant machine, dark blue with golden highlights, light up, mechanical parts clanking and churning. A red light came on and a message fired through space "….Decepticons, it is time."

Mike was glad to be able to rest for awhile. He loved his job, but saving the universe every couple years was tough as hell. Being able to take his crew (especially Miranda) out for a little break was nice. Everyone was enjoying themselves except, perhaps Grunt. He looked cross that his Varren skewers weren't raw and still bleeding. Garrus had stripped himself of his armor and took on more leisurely clothing. But the scars on the side of his face still drew plenty on looks from the crowds of this vastly populated and colorful world.

Last time he was here his team had been looking for Thane Krios, a famous Drell Assassin. Some of the things Nassana Dantius had done were horrific and unjust. Her paranoia leads her to kill her own works to "protect" herself. The frail Salarians were gunned down before they could even try to escape. It was horrific. The green gore splattering the walls, the screams and wheezes of the dying. The soft, amphibious skulls splattering like melons. He shivered. But there were also fond memories here was well. Helping Samara locate, saving Oriana, finding an Asari's love locket.

Shepard's mind stayed from these thoughts as he glanced around the beautiful city, the bright colors and the orange sunlight mixing to create an intoxicating haze. It was glorious. This warm world was amazing.

"Guys, I'm going to go see Liara. Anyone want to go?" said Mike, looking about. Garrus and Miranda complied, Miranda smiling slightly. She knew how important his friends were. Shepard would lay down his life for any of them, even uncivilized creatures like Jack. He was so fascinating, watching him work with others. Mike got to know his crew; he went out of his way to help.

She was going to be with him to be with him, but Garrus was going to see his old shipmate. They were never close, but Liara was a friendly face in this horror story of a universe.

Grunt, Mordin and the others decided to explore the shops and the Eternity Bar while Shepard went to visit his friend.

Deep space, on an uncharted world, construction on a base begins under the harsh white light of a meandering white dwarf. The base was being built deep underground and it was being shielded against any form of signal that could give them away.

A giant machine sat in a makeshift throne, his helmet-like head turned toward his wrist communicator. On his right arm, a massive cannon with enough fire power to make a Thanix cannon look like a spit ball shooter. He was huge and alien, hundreds of scars and burns coating his body with a large purple symbol on his chest. A large scar, a deep one he had never repaired, ran crossed his massive chest. It was a symbol, a symbol of what it cost to be free.

He received a signal, sent back by his communications expert. "….Decepticons, it is time." It played and a sadistic grin crawled acrossed his face.

"So, Liara, how's the hunt for the Shadow Broker been going?" said Shepard, leaning forward slightly. His friend had been hunting the mysterious information broker for a long time, in a quest for revenge.

"Not as well as I hoped, but better than I feared. Let's not spend all of our time with talk, Shepard. How are you and Ms. Williams doing?"

Mike gave her an uneasy look. Miranda raised an eyebrow. "Williams?" she said, a slight bit of veiled anger in her voice. She knew of Gunnery chief Ashley Williams, as she was part of Shepard's original crew. She did not know that there had once been something romantic between them. It was a pang of anger mixed with jealousy with a slight dash of curiosity.

"Liara, Ash moved on. She's different, I'm different. It's for the best." said Shepard, glancing at Miranda. Liara, thick as a brick, looked hopeful. She'd always harbored a crush on Mike, ever since his team freed her on Thurum.

"I'm with Miranda now." He said, looking at her. She gave him a look like "You have some serious explaining to do later."

Mike slumped slightly enough that only those staring at him intently would notice. He would have probably never have given Miranda a chance, except for the fact that Ashley, for all intensive purposes, had dumped him back on Horizon. He couldn't really blame her though, it had been two years and he was 'dead'. He felt shameful though, for clinging onto a new woman so quickly. He did have a lot of explaining to do, but he'd be more than happy to do it.

Miranda felt a chill creep through her heart. Was this other woman still a threat? More importantly, did Shepard still have feelings for her? She knew they weren't together anymore but still…it bothered her. She would talk to him once they got back to the ship. She'd never seen him lie, so she was confident he wouldn't start now.

"It is time to ruin the organics. To wipe their infection clean, galaxy by galaxy." Said the massive machine, standing at the heart of the base, his voice a cold and collected tone, very regal and full of class. Standing close by, his aerial commander.

"Rally the others. We have identified and located our enemy's current objective. We have much to do."

"Shepard, we need to talk." Said Miranda, sitting in front of him. She'd lead him up to his cabin.

"Miranda…I'm sorry. Ash and I have been done for a long time. I'm sorry I never mentioned it before…"Shepard slumped into the seat, defeated.

"You never talk about what happened between you and Jacob, either."

Miranda was slightly taken aback by this. She knew they seemed close, but how did Shepard…nevermind. She realized she wasn't giving him enough credit. She suddenly felt her superiority complex shrink back.

"I'm sorry, Mike." She whispered over the table, her hand reaching out. Now she felt like a real bitch. "I was just worried that…you know, may still have feelings for her…"

Mike touched her arm, a slight smile on his face. "Don't worry about it, Miranda. I love you…to tell you the truth though, when we first met, you seemed to hate me." Ashley would always be his friend, but after that stunt she pulled on Horizon, there was no going back. She turned her back on him…he wasn't particularly happy about that, but he wouldn't throw out their friendship so easily. She was good at heart, but Miranda saved his ass in more ways than one.

She slid around and sat next to him, her hand on his.

"Really? Why would I hate you?" she said, looking at him, a slightly puzzled look on her marvelously sculpted face, dark hair framing it in flowing locks.

"You just didn't seem very confident that I was worth the money and time Cerberus put into me. But after awhile, you started getting more and more comfortable around me. That part was abit funny." He said, shrugging his shoulders abit.

"How? And I never hated you. You had become more than an investment for me. It was almost an obsession for awhile. Finding everything there is to know…maybe my research wasn't as complete as I thought."

"It was good to see you smile. I thought it was funny because I thought of you as all business and no emotion. It was good to see you let your hair down abit. This may seem a little silly to ask now, but why did you give me a chance?" inquired Mike, putting his arm around her, pulling her close. Miranda rested her head on his shoulder.

"Saving Oriana, no question. You showed me a side few truly have, a selfless side. You even convinced me to talk to her about what was going on. As we kept going on missions and helping the others, I saw you in a new light. I began to like you…and I'll admit it, I was jealous of Tali. You seemed to like her, so I didn't say anything. But you kept coming to talk to me. It was strange, but I loved it. Why did you start liking me if I had been so cold to you?"

"I love getting to know my crew. It's very important to me and it keeps morale up. But, after talking with you a few times, you're icy exterior began to melt away and you began to show your truth colors. I wanted to know you better and I began to care about you. It was different than the others. The others, I would lay down my life for. You, I'd lay down much more for."

Miranda snuggled close to Shepard, close to his warm, hard body. It was so peaceful here, with him. Her mind slipped from all worries and fear. The Reapers were now just a distant memory.

"Miri, want to go out? Just you and me? We can go get some dinner." Said Shepard softly in year ear, tickling her.

"Sure. A little one on one time would be great." She said, smiling up at him.

"Decepticons, the Autobot's goal is on the organic world called Ilium. As we speak, the Seekers head towards them. Soon enough, the Autobots will be crushed, the organics will be wiped clean and the universe will be ours!" roared Megatron, raising his cannon arm up. The crowd of ancient machines before him cheered, the sound of dark mechanical monsters preparing for a slaughter. Their machines, the Reapers would be used as fodder, hurling them against the fleets of their foes. Oh, they could attack them directly, but why sacrifice men instead of worthless supply drones?

"It has been a long war. Most of us don't even remember what home looks like! Don't you want your protoforms to grow up knowing that you helped reclaim our true home? Soon enough men, we will win. We have too. This is a necessary war, to return us to glory!"

A mass effect warp opened and three vessels were expelled forth. One was red, blue and white, while one sported black and purple and the other solid blue. They were the true Seekers, not the silly swarms that the Collectors created. These Decepticons were vast and sleek, moving faster than any ship in known space.

"Ilium defense grid, please identify yourselves or we will fire." Came a cold female voice. Starscream took no notice of the puny creature's defenses. They couldn't hit him, let alone hurt him. In space, he was unparalleled. They were there to capture or terminate Shepard, no matter what the cost. This world would burn anyway. Might as well have fun with it first.

The ship insect's ships swarmed toward them, firing their puny weapons. Mass effect powered slugs hit them and flattened on their hardened armor. Lasers bounced off, having next to no effect on the ancient cybertronian warriors.

"Skywarp, Thundercracker, take them out. I'm going groundside." Hissed the air commander, his jets firing at full capacity.

"Mike, this place, wow. I'm surprised, no one's ever…" said Miranda, looking into the vast, colorful expanse before her. The restaurant looked like a small city, it was massive.

"Don't worry about it. I'd do anything for you." He said, squeezing her hand lightly.

Shepard was like all the best things humanity had to offer all rolled into one being. He was totally selfless, kind, caring…cute. She felt like melting around him, his air of kindness and strength. She felt safe with him. Miranda was almost dumb struck by him. He was just so damn different than anyone she'd ever met. He was dependable and never lied.

Thundercracker twisted and looped, dodging fire but not really returning it. He was forced into Decepticon service long ago and had stuck with his brothers. He had ideals and slaughtering helpless organic creatures that were identified as Asari were not in them. Skywarp on the other hand, loved it. He teleported about, causing the defense force become confused. He'd pop up behind a ship and fire his deep purple null ray and blow the vessel apart like it was tissue paper.

"These creatures annoy me." He spat, his voice filled with contempt. He had transformed into his true form, a sleek alien machine designed for death.

"The dinner's wonderful, Mike. Thank you." Said Miranda, holding her drink lightly.

"Don't thank me. It's way over due."

A loud, resounding boom echoed out over the city, a massive explosion ripping a building acrossed the city apart. All races were stunned, many screamed in terror as thousands of tons of concrete and steel rained into the streets. A cloud of dust and debris raged, chocking the helpless and blinding. A sickening laugh came out of the burning buildings heart and a gigantic creature flew, still alight, out of it. The machine was almost as tall as the building itself! It laughed again, firing a purple heat ray through the streets, incinerating the powerless people of Nos Astra. People closest to the heart of the beam were vaporized, while others turned into bloody, running liquid, filling the drains. People screamed and children clung to their mothers, praying for relief. Starscream swept the ray acrossed a building, cutting it in half horizontally.

"Shepard!" it roared out.

"Mike! What the hell is that?!" screamed Miranda, gripping him. That was unusual, for her any way. But, holy hell! What the fuck was that? And how did it know him?

"I know you're here, human! Give yourself up!" the machine thundered. It turned and began scanning about, red eyes in the twilight of the darkening world as the sun began to set. The burning building highlighted the robot, the flames glinting off its metal skin.

"We have to get back to the Normandy, Shepard. This thing obviously wants you." Said Miranda, pulling Mike up. They began to run, the streets crowding with the terror struck citizens of the city. It was lucky that they were so close to the docking port.

The couple ran, navigating their way through a thick torrent of crazed aliens, all trying to evade a monstrous engine of destruction, the likes of which they'd never known.

Starscream's acute vision tuned in, he spotted the ship that was identified as Shepard's. "Best not to let Megatron get his hands on…whatever makes 'Shepard' important." Thought Starscream, charging his null ray. He fired, the blast missing by a fraction of a centimeter and slamming into a building just beyond it. The collapsing building fell toward the Normandy, which had been knocked offline when he fired the null ray. The null ray was not only vastly destructive, but it also produced a prodigious EMP wave.

"Mike!" screamed Miranda, glancing over at the collapsing building. Chucks of concrete fell about. Damnit, they were so close! A metal clanking and a strange, alien sound filled the air. They both expected to be vaporized-

"Shepard!" Yelled a thunderous voice from above. It sounded like God himself was talking to them. They looked up and a massive machine had pressed its back to the building. A gigantic hand with an open port was in front of them. "Shepard, go! It's safe." Said the machine, his face plate moving. Two large antenna like structures stood to either side of his head.

The machine looked ancient, perhaps Reaper ancient. Its body was covered in scars and welds holding things together. A few intricate glyphs stood out on its red and blue armored skin. The robot was huge, massive enough to bear the weight of a skyscraper leaning on it. It shoved upwards with its shoulders, knocking the building in the other direction.

"Joker? Joker?! Damn, just static!" yelled Shepard.

"Prime?" snarled the Seeker, turning to see his ancient foe.

"Starscream, cease this slaughter now!" roared the massive Autobot.

There was obscene laughter, cackling as he fired his ray into the crowds, melting them into oily stains on the streets, running like water.

The giant above them looked down with glass eyes, lighting blue from within, but they seemed deeper than that, soulful. "Get to your ship. I'll hold him here."

"Mike, let's go." Said Miranda softly, still in awe of the whole situation. They ran towards the Normandy, both of them still thinking "What the fuck is going on?"

The Seeker lifted up on plasma jet engines and fired himself forward. Optimus drew his ion rifle, preparing to fire. There was a flash of light behind him and Skywarp emerged from a portal, slamming into the ancient leader.

The purple and black fighter gripped on to him, trying to keep the giant still. Optimus reached back and grasped him by his elongated Decepticon head and hurled him forward, over his shoulder into the oncoming Starscream. "This ends here." Growled Optimus, assuming a fighters stance in the ruined city.

The Normandy blasted up, piercing the planet's atmosphere. Once in space, Joker said "These trips are fun and all, but what the hell commander? Every ten minutes some warped freaky alien or mighty machine wants to kill us. Care to explain?"

"You know as much as I do, Joker. But those things are fighting and one of them saved my a- check those readings, the unknowns from the other day and run them against the creatures down there. There has to be a link."

Around them, there were the wrecked hulls of the defender's ships. Something had laid ruin to them, probably that giant machine "Starscream". Suddenly, the radio started buzzing. A message came through, a set of coordinates. The voice was "Optimus's!"

"Joker, set that course into motion. He saved my ass and I want to know just what the hell is going on."

"You sure that's wise commander? We don't know what the tin cans want. What if they want information or something?"

"Then I'll deal with it when I have too." Said Shepard, turning toward Miranda. She looked shaken, to say the least. She'd seen plenty of death, but that was something different. That thing was enjoying it. It liked just melting the innocent, like a sadistic child frying ants. There was no reason for it, no reason at all.

"Course set commander. We should be there in just under two hours, provided something doesn't blow us up." Said Joker.

Yeah. This was tough and I did multiple versions. I warned of a crossover at the beginning, so if it's off putting, I'm sorry. Please review, I like to know my mistakes so I may fix them in the future.


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